arXiv subjects

Michael F. Hagan

Publications and source records attributed to Michael F. Hagan.

At least 55 records · Page 3Linked to original sources

arXiv2019

Response of active Brownian particles to boundary driving

We computationally study the behavior of underdamped active Brownian particles in a sheared channel geometry. Due to their underdamped dynamics, the particles carry momentum a characteristic distance away from the boundary before it is dissipated into the substrate. We correlate this distance with the persistence of particle trajectories, determined jointly by their friction and self-propulsion. Within this characteristic length, we observe new and counterintuitive phenomena stemming from the interplay of activity, interparticle interactions, and the boundary driving. Depending on values of friction and self-propulsion, interparticle interactions can either aid or hinder momentum transport. More dramatically, in certain cases we observe a flow reversal near the wall, which we correlate with an induced polarization of the particle self-propulsion directions. We rationalize these results in terms of a simple kinetic picture of particle trajectories.

cond-mat.soft↗

arXiv2019

The role of the encapsulated cargo in microcompartment assembly

Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform dynamical simulations of shell assembly in the presence and absence of cargo over a range of interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell relative to its intrinsic spontaneous curvature, as seen in recent experiments. These features are controlled by a balance of kinetic and thermodynamic effects, and the shell size is assembly pathway dependent. We discuss implications of these results for synthetic biology efforts to target new enzymes to microcompartment interiors.

physics.bio-ph↗

arXiv2019

Conformational switching of chiral colloidal rafts regulates raft-raft attractions and repulsions

Membrane-mediated particle interactions depend both on the properties of the particles themselves and the membrane environment in which they are suspended. Experiments have shown that chiral rod-like inclusions dissolved in a colloidal membrane of opposite handedness assemble into colloidal rafts, which are finite-sized reconfigurable droplets consisting of a large but precisely defined number of rods. Here, we systematically tune the chirality of the background membrane, and find that in the achiral limit colloidal rafts acquire fundamentally new structural properties and interactions. In particular, rafts can switch between two chiral states of opposite handedness, which dramatically alters the nature of the membrane-mediated raft-raft interactions. Rafts with the same chirality have long-ranged repulsions, while those with opposite chirality acquire attractions with a well-defined minimum. Both attractive and repulsive interactions are explained by a continuum model that accounts for the coupling between the membrane thickness and the local tilt of the constituent rods. These switchable interactions enable assembly of colloidal rafts into intricate higher-order architectures with unusual symmetries, including stable tetrameric clusters and "ionic crystallites" of counter-twisting domains organized on a binary square lattice. Furthermore, the properties of individual rafts, such as their sizes, are controlled by their complexation with other rafts. The emergence of these complex behaviors can be rationalized purely in terms of generic couplings between compositional and orientational order of fluids of rod-like elements. Thus, the uncovered principles might have relevance for conventional lipid bilayers, in which the assembly of higher-order structures is also mediated by complex membrane-mediated interactions.

cond-mat.soft↗

arXiv2018

Nanoparticles Binding to Lipid Membranes: from Vesicle-Based Gels to Vesicle Inversion and Destruction

Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of examples, we still lack the design principles to control membrane morphology in synthetic systems. Here we show that even the relatively simple case of spherical nanoparticles binding to lipid-bilayer membrane vesicles results in a remarkably rich set of morphologies that can be controlled quantitatively via the particle binding energy. We find that when the binding energy is weak relative to a characteristic membrane-bending energy, the vesicles adhere to one another and form a soft solid, which could be used as a useful platform for controlled release. When the binding energy is larger, the vesicles undergo a remarkable destruction process consisting first of invaginated tubules, followed by vesicles turning inside-out, yielding a network of nanoparticle-membrane tubules. We propose that the crossover from one behavior to the other is triggered by the transition from partial to complete wrapping of nanoparticles. This model is confirmed by computer simulations and by quantitative estimates of the binding energy. These findings open the door to a new class of vesicle-based, closed-cell gels that are more than 99% water and can encapsulate and release on demand. Our results also show how to intentionally drive dramatic shape changes in vesicles as a step toward shape-responsive particles. Finally, they help us to unify the wide range of previously observed responses of vesicles and cells to added nanoparticles.

cond-mat.soft↗

arXiv2017

Why enveloped viruses need cores -- the contribution of a nucleocapsid core to viral budding

During the alphavirus lifecycle, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of infectious particles. To determine the role of the nucleocapsid core, we develop a coarse-grained computational model with which we investigate budding dynamics as a function of glycoprotein and nucleocapsid interactions, as well as budding in the absence of a nucleocapsid. We find that there is a transition between glycoprotein-directed budding and nucleocapsid-directed budding which occurs above a threshold strength of nucleocapsid interactions. The simulations predict that glycoprotein-directed budding leads to significantly increased size polydispersity and particle polymorphism. This polydispersity can be qualitatively explained by a theoretical model accounting for the competition between bending energy of the membrane and the glycoprotein shell. The simulations also show that the geometry of a budding particle leads to a barrier to subunit diffusion, which can result in a stalled, partially budded state. We present a phase diagram for this and other morphologies of budded particles. Comparison of these structures against experiments could establish bounds on whether budding is directed by glycoprotein or nucleocapsid interactions. Although our model is motivated by alphaviruses, we discuss implications of our results for other enveloped viruses.

physics.bio-ph↗

arXiv2017

Steady-state distributions of ideal active Brownian particles under confinement and forcing

We develop a formally exact technique for obtaining steady-state distributions of non-interacting active Brownian particles in a variety of systems. Our technique draws on results from the theory of two-way diffusion equations to solve the steady-state Smoluchowski equation for the 1-particle distribution function. The methods are employed to study in detail three scenarios: 1) confinement in a channel, 2) a constant flux steady state, and 3) sedimentation in a uniform external field. In each scenario, known behaviors are reproduced and precisely quantified, and new results are presented. In particular, in the constant flux state we derive an effective diffusivity which interpolates between the ballistic behavior of particle trajectories at short distances and their diffusive behavior at large distances. We also calculate the sedimentation profile of active Brownian particles near a wall, which complements earlier studies on the part far from the wall. Our techniques easily generalize to other active models, including systems whose activity is modeled in terms of Gaussian colored noise.

cond-mat.soft↗

arXiv2016

Equilibrium mappings in polar-isotropic confined active particles

Despite their fundamentally non-equilibrium nature, the individual and collective behavior of active systems with polar propulsion and isotropic interactions (polar-isotropic active systems) are remarkably well captured by equilibrium mapping techniques. Here we examine two signatures of equilibrium systems -- the existence of a local free energy function and the independence of the coarse- grained behavior on the details of the microscopic dynamics -- in polar-isotropic active particles confined by hard walls of arbitrary geometry at the one-particle level. We find that boundaries that possess concave regions make the density profile strongly dynamics-dependent and give it a nonlocal dependence on the geometry of the confining box. This in turn constrains the scope of equilibrium mapping techniques in polar-isotropic active systems.

cond-mat.soft↗

arXiv2016

A classical nucleation theory description of active colloid assembly

Non-aligning self-propelled particles with purely repulsive excluded volume interactions undergo athermal motility-induced phase separation into a dilute gas and a dense cluster phase. Here, we use enhanced sampling computational methods and analytic theory to examine the kinetics of formation of the dense phase. Despite the intrinsically nonequilibrium nature of the phase transition, we show that the kinetics can be described using an approach analogous to equilibrium classical nucleation theory, governed by an effective free energy of cluster formation with identifiable bulk and surface terms. The theory captures the location of the binodal, nucleation rates as a function of supersaturation, and the cluster size distributions below the binodal, while discrepancies in the metastable region reveal additional physics about the early stages of active crystal formation. The success of the theory shows that a framework similar to equilibrium thermodynamics can be obtained directly from the microdynamics of an active system, and can be used to describe the kinetics of evolution toward nonequilibrium steady states.

cond-mat.soft↗

arXiv2016

Recent advances in coarse-grained modeling of virus assembly

In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical processes. We present an overview of recent technological and algorithmic developments, which are enabling simulations to describe the large ranges of length-and time-scales relevant to assembly, under conditions more closely matched to experiments than in earlier work. We then describe two examples in which computational modeling has recently provided an important complement to experiments.

q-bio.BM↗

arXiv2016

Faceted particles formed by the frustrated packing of anisotropic colloids on curved surfaces

We use computer simulations and simple theoretical models to analyze the morphologies that result when rod-like particles end-attach onto a curved surface, creating a finite-thickness monolayer aligned with the surface normal. This geometry leads to two forms of frustration, one associated with the incompatibility of hexagonal order on surfaces with Gaussian curvature, and the second reflecting the deformation of a layer with finite thickness on a surface with non-zero mean curvature. We show that the latter effect leads to a faceting mechanism. Above threshold values of the inter-particle attraction strength and surface mean curvature, the adsorbed layer undergoes a transition from orientational disorder to an ordered state that is demarcated by reproducible patterns of line defects. The number of facets is controlled by the competition between line defect energy and intra-facet strain. Tuning control parameters thus leads to a rich variety of morphologies, including icosahedral particles and irregular polyhedra. In addition to suggesting a new strategy for the synthesis of aspherical particles with tunable symmetries, our results may shed light on recent experiments in which rod-like HIV GAG proteins assemble around nanoscale particles.

cond-mat.soft↗

arXiv2016

Allosteric control in icosahedral capsid assembly

During the lifecycle of a virus, viral proteins and other components self-assemble to form a symmetric protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data.

q-bio.SC↗

arXiv2016

Theory of microphase separation in bidisperse chiral membranes

We present a Ginzburg-Landau theory of micro phase separation in a bidisperse chiral membrane consisting of rods of opposite handendness. This model system undergoes a phase transition from an equilibrium state where the two components are completely phase separated to a microphase separated state composed of domains of a finite size comparable to the twist penetration depth. Characterizing the phenomenology using linear stability analysis and numerical studies, we trace the origin of the discontinuous change in domain size that occurs during this to a competition between the cost of creating an interface and the gain in twist energy for small domains in which the twist penetrates deep into the center of the domain.

cond-mat.soft↗

arXiv2016

The Allosteric Switching Mechanism in Bacteriophage MS2

In this article we use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopt different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

physics.bio-ph↗

arXiv2016

Emergent Self-organization in Active Materials

Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium materials, with emergent properties comparable to those of living systems. This review will describe two recently developed classes of active matter systems, in which simple building blocks --- self-propelled colloidal particles or extensile rod-like particles --- self-organize to form macroscopic structures with features not possible in equilibrium systems. We summarize the recent experimental and theoretical progress on each of these systems, and we present simple descriptions of the physics underlying their emergent behaviors.

cond-mat.soft↗

arXiv2016

Interaction of chiral rafts in self-assembled colloidal membranes

Colloidal membranes are monolayer assemblies of rodlike particles that capture the long-wavelength properties of lipid bilayer membranes on the colloidal scale. Recent experiments on colloidal membranes formed by chiral rodlike viruses showed that introducing a second species of virus with different length and opposite chirality leads to the formation of rafts --- micron-sized domains of one virus species floating in a background of the other viruses [Sharma et al., Nature 513, 77 (2014)]. In this article we study the interaction of such rafts using liquid crystal elasticity theory. By numerically minimizing the director elastic free energy, we predict the tilt angle profile for both a single raft and two rafts in a background membrane, and the interaction between two rafts as a function of their separation. We find that the chiral penetration depth in the background membrane sets the scale for the range of the interaction. We compare our results with the experimental data and find good agreement for the strength and range of the interaction. Unlike the experiments, however, we do not observe a complete collapse of the data when rescaled by the tilt angle at the raft edge.

cond-mat.soft↗

arXiv2016

Active Particles on Curved Surfaces

Recent studies have highlighted the sensitivity of active matter to boundaries and their geometries. Here we develop a general theory for the dynamics and statistics of active particles on curved surfaces and illustrate it on two examples. We first show that active particles moving on a surface with no ability to probe its curvature only exhibit steady-state inhomogeneities in the presence of orientational order. We then consider a strongly confined 3D ideal active gas and compute its steady-state density distribution in a box of arbitrary convex shape.

cond-mat.soft↗

arXiv2016

Dynamics and density distribution of strongly confined noninteracting nonaligning self-propelled particles in a nonconvex boundary

We study the dynamics of non-aligning, non-interacting self-propelled particles confined to a box in two dimensions. In the strong confinement limit, when the persistence length of the active particles is much larger than the size of the box, particles stay on the boundary and align with the local boundary normal. It is then possible to derive the steady-state density on the boundary for arbitrary box shapes. In non-convex boxes, the non-uniqueness of the boundary normal results in hysteretic dynamics and the density is non-local, i.e. it depends on the global geometry of the box. These findings establish a general connection between the geometry of a confining box and the behavior of an ideal active gas it confines, thus providing a powerful tool to understand and design such confinements.

cond-mat.soft↗

arXiv2015

Probing a self-assembled fd virus membrane with a microtubule

The self-assembly of highly anisotropic colloidal particles leads to a rich variety of morphologies, whose properties are just beginning to be understood. This article uses computer simulations to probe a particle-scale perturbation of a commonly studied colloidal assembly, a monolayer membrane composed of rodlike fd viruses in the presence of a polymer depletant. Motivated by experiments currently in progress, we simulate the interaction between a microtubule and a monolayer membrane as the microtubule "pokes" and penetrates the membrane face-on. Both the viruses and the microtubule are modeled as hard spherocylinders of the same diameter, while the depletant is modeled using ghost spheres. We find that the force exerted on the microtubule by the membrane is zero either when the microtubule is completely outside the membrane or when it has fully penetrated the membrane. The microtubule is initially repelled by the membrane as it begins to penetrate but experiences an attractive force as it penetrates further. We assess the roles played by translational and rotational fluctuations of the viruses and the osmotic pressure of the polymer depletant. We find that rotational fluctuations play a more important role than the translational ones. The dependence on the osmotic pressure of the depletant of the width and height of the repulsive barrier and the depth of the attractive potential well is consistent with the assumed depletion-induced attractive interaction between the microtubule and viruses. We discuss the relevance of these studies to the experimental investigations. \end{abstract}

cond-mat.soft↗